Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3)

• Published in: Journal of molecular biology Vol. 394; no. 4; pp. 644 - 652
• Main Authors: Jeong, Haeyoung, Barbe, Valérie, Lee, Choong Hoon, Vallenet, David, Yu, Dong Su, Choi, Sang-Haeng, Couloux, Arnaud, Lee, Seung-Won, Yoon, Sung Ho, Cattolico, Laurence, Hur, Cheol-Goo, Park, Hong-Seog, Ségurens, Béatrice, Kim, Sun Chang, Oh, Tae Kwang, Lenski, Richard E., Studier, F. William, Daegelen, Patrick, Kim, Jihyun F.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 11.12.2009
• Subjects: BL21(DE3); Comparative genomics; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; E. coli B; Escherichia coli; Escherichia coli - genetics; Genome, Bacterial; Interspersed Repetitive Sequences; Molecular Sequence Data; Polymorphism, Genetic; Prophages - genetics; REL606; Sequence Analysis, DNA; Shigella; Similarity of E. coli B and K-12; BL21(DE3); Similarity of E. coli B and K-12; SNP; Comparative genomics; E. coli B; LPS; REL606
• ISSN: 0022-2836; 1089-8638; 1089-8638
• DOI: 10.1016/j.jmb.2009.09.052

Escherichia coli K-12 and B have been the subjects of classical experiments from which much of our understanding of molecular genetics has emerged. We present here complete genome sequences of two E. coli B strains, REL606, used in a long-term evolution experiment, and BL21(DE3), widely used to express recombinant proteins. The two genomes differ in length by 72,304 bp and have 426 single base pair differences, a seemingly large difference for laboratory strains having a common ancestor within the last 67 years. Transpositions by IS1 and IS150 have occurred in both lineages. Integration of the DE3 prophage in BL21(DE3) apparently displaced a defective prophage in the λ attachment site of B. As might have been anticipated from the many genetic and biochemical experiments comparing B and K-12 over the years, the B genomes are similar in size and organization to the genome of E. coli K-12 MG1655 and have >99% sequence identity over ∼92% of their genomes. E. coli B and K-12 differ considerably in distribution of IS elements and in location and composition of larger mobile elements. An unexpected difference is the absence of a large cluster of flagella genes in B, due to a 41 kbp IS1-mediated deletion. Gene clusters that specify the LPS core, O antigen, and restriction enzymes differ substantially, presumably because of horizontal transfer. Comparative analysis of 32 independently isolated E. coli and Shigella genomes, both commensals and pathogenic strains, identifies a minimal set of genes in common plus many strain-specific genes that constitute a large E. coli pan-genome.